"Benito Cereno" seems to be a weird choice for the title, right? After all, it's not Benito himself who's running the show (that would be Babo) or even acting as the protagonist (that would be Delano). Cereno is just… enigmatic.
But consider that this story was written by Herman Melville, who has a habit of titling his works after the central enigma in the story—think Moby Dick. Much like the white whale, Cereno is the figure upon which all the other characters pin their hopes and identities. The slaves aspire to be Cereno—free and in charge. Delano aspires to both help Cereno and figure out what his deal is.
Also, like the title Moby Dick, "Benito Cereno" is intentionally confusing. It raises doubt as to who the protagonist and hero of the story is, or even, indeed, if there is a hero. When you read a 19th Century novel like Jane Eyre, for example, you rest easy knowing that Jane Eyre herself is the protagonist. She's right there in the title!
But Meville—who likes fiddling with nuances and gray areas—picks the weakest, most impotent character in the story to use as the titular figure. This could be his way of saying, "Abandon hope of heroes, all ye who enter here."